Numerical algebraic geometry for model selection and its application to the life sciences

Researchers working with mathematical models are often confronted by the related problems of parameter estimation, model validation, and model selection. These are all optimization problems, well-known to be challenging due to non-linearity, non-convexity and multiple local optima. Furthermore, the challenges are compounded when only partial data is available. Here, we consider polynomial models (e.g., mass-action chemical reaction networks at steady state) and describe a framework for their analysis based on optimization using numerical algebraic geometry. Specifically, we use probability-one polynomial homotopy continuation methods to compute all critical points of the objective function, then filter to recover the global optima. Our approach exploits the geometric structures relating models and data, and we demonstrate its utility on examples from cell signaling, synthetic biology, and epidemiology.Comment: References added, additional clarification

Algorithms for Mappings and Symmetries of Differential Equations

Differential Equations are used to mathematically express the laws of physics and models in biology, finance, and many other fields. Examining the solutions of related differential equation systems helps to gain insights into the phenomena described by the differential equations. However, finding exact solutions of differential equations can be extremely difficult and is often impossible. A common approach to addressing this problem is to analyze solutions of differential equations by using their symmetries. In this thesis, we develop algorithms based on analyzing infinitesimal symmetry features of differential equations to determine the existence of invertible mappings of less tractable systems of differential equations (e.g., nonlinear) into more tractable systems of differential equations (e.g., linear). We also characterize features of the map if it exists. An algorithm is provided to determine if there exists a mapping of a non-constant coefficient linear differential equation to one with constant coefficients. These algorithms are implemented in the computer algebra language Maple, in the form of the MapDETools package. Our methods work directly at the level of systems of equations for infinitesimal symmetries. The key idea is to apply a finite number of differentiations and eliminations to the infinitesimal symmetry systems to yield them in the involutive form, where the properties of Lie symmetry algebra can be explored readily without solving the systems. We also generalize such differential-elimination algorithms to a more frequently applicable case involving approximate real coefficients. This contribution builds on a proposal by Reid et al. of applying Numerical Algebraic Geometry tools to find a general method for characterizing solution components of a system of differential equations containing approximate coefficients in the framework of the Jet geometry. Our numeric-symbolic algorithm exploits the fundamental features of the Jet geometry of differential equations such as differential Hilbert functions. Our novel approach establishes that the components of a differential equation can be represented by certain points called critical points

The complexity of the nucleolus in compact games

This is the author accepted manuscript. The final version is available from ACM via the DOI in this recordThe nucleolus is a well-known solution concept for coalitional games to fairly distribute the total available worth among the players. The nucleolus is known to be NP-hard to compute over compact coalitional games, that is, over games whose functions specifying the worth associated with each coalition are encoded in terms of polynomially computable functions over combinatorial structures. In particular, hardness results have been exhibited over minimum spanning tree games, threshold games, and flow games. However, due to its intricate definition involving reasoning over exponentially many coalitions, a nontrivial upper bound on its complexity was missing in the literature and looked for. This article faces this question and precisely characterizes the complexity of the nucleolus, by exhibiting an upper bound that holds on any class of compact games, and by showing that this bound is tight even on the (structurally simple) class of graph games. The upper bound is established by proposing a variant of the standard linear-programming based algorithm for nucleolus computation and by studying a framework for reasoning about succinctly specified linear programs, which are contributions of interest in their own. The hardness result is based on an elaborate combinatorial reduction, which is conceptually relevant for it provides a "measure" of the computational cost to be paid for guaranteeing voluntary participation to the distribution process. In fact, the pre-nucleolus is known to be efficiently computable over graph games, with this solution concept being defined as the nucleolus but without guaranteeing that each player is granted with it at least the worth she can get alone, that is, without collaborating with the other players. Finally, this article identifies relevant tractable classes of coalitional games, based on the notion of type of a player. Indeed, in most applications where many players are involved, it is often the case that such players do belong in fact to a limited number of classes, which is known in advance and may be exploited for computing the nucleolus in a fast way.Part of E. Malizia’s work was supported by the European Commission through the European Social Fund and by Calabria Regio

An Overview of Fairness Notions in Multi-Party Computation

Die sichere Mehrparteienberechnung (``Multi-party Computation\u27\u27, MPC) ist eine kryptografische Technik, die es mehreren Parteien, die sich gegenseitig misstrauen, ermöglicht, gemeinsam eine Funktion über ihre privaten Eingaben zu berechnen. Fairness in MPC ist definiert als die Eigenschaft, dass, wenn eine Partei die Ausgabe erhält, alle ehrlichen Parteien diese erhalten. Diese Arbeit befasst sich mit dem Defizit an umfassenden Übersichten über verschiedene Fairnessbegriffe in MPC. Vollständige Fairness (``complete fairness\u27\u27), die oft als Ideal angesehen wird, garantiert, dass entweder alle ehrlichen Parteien ein Ergebnis erhalten oder keine. Dieses Ideal ist jedoch aufgrund theoretischer und kontextbezogener Beschränkungen im Allgemeinen nicht zu erreichen. Infolgedessen haben sich alternative Begriffe herausgebildet, um diese Einschränkungen zu überwinden. In dieser Arbeit werden verschiedene Fairnessbegriffe in MPC untersucht, darunter vollständige Fairness, partielle Fairness (``Partial Fairness\u27\u27), Delta-Fairness, graduelle Freigabe, Fairness mit Strafen und probabilistische Fairness. Jedes Konzept stellt unterschiedliche Anforderungen und Einschränkungen für reale Szenarien dar. Wir stellen fest, dass vollständige Fairness eine ehrliche Mehrheit erfordert, um für allgemeine Funktionen ohne stärkere Annahmen, wie z. B. den Zugang zu öffentlichen Ledgern, erreicht zu werden, während bestimmte Funktionen auch ohne diese Annahmen mit vollständiger Fairness berechnet werden können. Andere Begriffe, wie Delta-Fairness, erfordern sichere Hardwarekomponenten. Wir geben einen Überblick über die Begriffe, ihre Zusammenhänge, Kompromisse und praktischen Implikationen dieser Begriffe. Darüber hinaus fassen wir die Ergebnisse in einer vergleichenden Tabelle zusammen, die einen kompakten Überblick über die Protokolle bietet, die diese Fairnessbegriffe erfüllen, und die Kompromisse zwischen Sicherheit, Effizienz und Anwendbarkeit aufzeigt. In der Arbeit werden Annahmen und Einschränkungen im Zusammenhang mit verschiedenen Fairnessbegriffe aufgezeigt und Protokolle aus grundlegenden Arbeiten auf diesem Gebiet zitiert. Es werden auch mehrere Unmöglichkeitsergebnisse vorgestellt, die die inhärenten Herausforderungen beim Erreichen von Fairness im MPC aufzeigen. Die praktischen Implikationen dieser Fairnesskonzepte werden untersucht und geben Einblicke in ihre Anwendbarkeit und Grenzen in realen Szenarien

Complexity Theory, Game Theory, and Economics: The Barbados Lectures

This document collects the lecture notes from my mini-course "Complexity Theory, Game Theory, and Economics," taught at the Bellairs Research Institute of McGill University, Holetown, Barbados, February 19--23, 2017, as the 29th McGill Invitational Workshop on Computational Complexity. The goal of this mini-course is twofold: (i) to explain how complexity theory has helped illuminate several barriers in economics and game theory; and (ii) to illustrate how game-theoretic questions have led to new and interesting complexity theory, including recent several breakthroughs. It consists of two five-lecture sequences: the Solar Lectures, focusing on the communication and computational complexity of computing equilibria; and the Lunar Lectures, focusing on applications of complexity theory in game theory and economics. No background in game theory is assumed.Comment: Revised v2 from December 2019 corrects some errors in and adds some recent citations to v1 Revised v3 corrects a few typos in v

Witnessing eigenstates for quantum simulation of Hamiltonian spectra

The efficient calculation of Hamiltonian spectra, a problem often intractable on classical machines, can find application in many fields, from physics to chemistry. Here, we introduce the concept of an "eigenstate witness" and through it provide a new quantum approach which combines variational methods and phase estimation to approximate eigenvalues for both ground and excited states. This protocol is experimentally verified on a programmable silicon quantum photonic chip, a mass-manufacturable platform, which embeds entangled state generation, arbitrary controlled-unitary operations, and projective measurements. Both ground and excited states are experimentally found with fidelities >99%, and their eigenvalues are estimated with 32-bits of precision. We also investigate and discuss the scalability of the approach and study its performance through numerical simulations of more complex Hamiltonians. This result shows promising progress towards quantum chemistry on quantum computers.Comment: 9 pages, 4 figures, plus Supplementary Material [New version with minor typos corrected.

The Structure of Differential Invariants and Differential Cut Elimination

The biggest challenge in hybrid systems verification is the handling of differential equations. Because computable closed-form solutions only exist for very simple differential equations, proof certificates have been proposed for more scalable verification. Search procedures for these proof certificates are still rather ad-hoc, though, because the problem structure is only understood poorly. We investigate differential invariants, which define an induction principle for differential equations and which can be checked for invariance along a differential equation just by using their differential structure, without having to solve them. We study the structural properties of differential invariants. To analyze trade-offs for proof search complexity, we identify more than a dozen relations between several classes of differential invariants and compare their deductive power. As our main results, we analyze the deductive power of differential cuts and the deductive power of differential invariants with auxiliary differential variables. We refute the differential cut elimination hypothesis and show that, unlike standard cuts, differential cuts are fundamental proof principles that strictly increase the deductive power. We also prove that the deductive power increases further when adding auxiliary differential variables to the dynamics

IST Austria Technical Report

We consider the quantitative analysis problem for interprocedural control-flow graphs (ICFGs). The input consists of an ICFG, a positive weight function that assigns every transition a positive integer-valued number, and a labelling of the transitions (events) as good, bad, and neutral events. The weight function assigns to each transition a numerical value that represents ameasure of how good or bad an event is. The quantitative analysis problem asks whether there is a run of the ICFG where the ratio of the sum of the numerical weights of good events versus the sum of weights of bad events in the long-run is at least a given threshold (or equivalently, to compute the maximal ratio among all valid paths in the ICFG). The quantitative analysis problem for ICFGs can be solved in polynomial time, and we present an efficient and practical algorithm for the problem. We show that several problems relevant for static program analysis, such as estimating the worst-case execution time of a program or the average energy consumption of a mobile application, can be modeled in our framework. We have implemented our algorithm as a tool in the Java Soot framework. We demonstrate the effectiveness of our approach with two case studies. First, we show that our framework provides a sound approach (no false positives) for the analysis of inefficiently-used containers. Second, we show that our approach can also be used for static profiling of programs which reasons about methods that are frequently invoked. Our experimental results show that our tool scales to relatively large benchmarks, and discovers relevant and useful information that can be used to optimize performance of the programs